mise en page de xgb.plot.tree en r

Question

je suis en train de lire un XGB notebook et la commande xgb.plot.tree dans l'exemple résultat dans une image comme ceci:

Cependant quand je fais la même chose que je suis un pic comme ceci qui sont deux graphiques séparés et dans des couleurs différentes aussi.

Est-ce normal? sont les deux graphiques deux arbres?

Answer 1

J'ai le même problème. Selon un cas de problème sur le référentiel github xgboost, cela peut être dû à une modification de la bibliothèque DiagrammeR utilisée par xgboost pour le rendu des arbres. https://github.com/dmlc/xgboost/issues/2640

Au lieu de modifier l'objet « dgr_graph » avec des commandes Diagrammer, je choisis pour créer une nouvelle version du xgb.plot.tree de fonction qui définit la couleur de police de noeuds directement. Il suffisait d'ajouter le paramètre fontcolor="black" dans la ligne nodes <- DiagrammeR::create_node_df

xgb.plot.tree <- function (feature_names = NULL, model = NULL, n_first_tree = NULL, 
     plot_width = NULL, plot_height = NULL, ...) 
    { 

     if (class(model) != "xgb.Booster") { 
      stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.") 
     } 
     if (!requireNamespace("DiagrammeR", quietly = TRUE)) { 
      stop("DiagrammeR package is required for xgb.plot.tree", 
       call. = FALSE) 
     } 
     allTrees <- xgb.model.dt.tree(feature_names = feature_names, 
      model = model, n_first_tree = n_first_tree) 
     allTrees[, `:=`(label, paste0(Feature, "\\nCover: ", Cover, 
      "\\nGain: ", Quality))] 
     allTrees[, `:=`(shape, "rectangle")][Feature == "Leaf", `:=`(shape, 
      "oval")] 
     allTrees[, `:=`(filledcolor, "Beige")][Feature == "Leaf", 
      `:=`(filledcolor, "Khaki")] 
     nodes <- DiagrammeR::create_node_df(n = length(allTrees[, 
      ID] %>% rev), label = allTrees[, label] %>% rev, style = "filled", 
      color = "DimGray", fillcolor = allTrees[, filledcolor] %>% 
       rev, shape = allTrees[, shape] %>% rev, data = allTrees[, 
       Feature] %>% rev, fontname = "Helvetica", fontcolor="black") 
     edges <- DiagrammeR::create_edge_df(from = match(allTrees[Feature != 
      "Leaf", c(ID)] %>% rep(2), allTrees[, ID] %>% rev), to = match(allTrees[Feature != 
      "Leaf", c(Yes, No)], allTrees[, ID] %>% rev), label = allTrees[Feature != 
      "Leaf", paste("<", Split)] %>% c(rep("", nrow(allTrees[Feature != 
      "Leaf"]))), color = "DimGray", arrowsize = "1.5", arrowhead = "vee", 
      fontname = "Helvetica", rel = "leading_to") 
     graph <- DiagrammeR::create_graph(nodes_df = nodes, edges_df = edges) 
     DiagrammeR::render_graph(graph, width = plot_width, height = plot_height) 
    } 

Then, it remains to change some parameters to improve the readibility of the graph. Below I add an example of the code I use to display the first tree of my xgboost model. 

    xgb.plot.tree <- function (feature_names = NULL, model = NULL, n_first_tree = NULL, 
     plot_width = NULL, plot_height = NULL, ...) 
    { 

     if (class(model) != "xgb.Booster") { 
      stop("model: Has to be an object of class xgb.Booster model generaged by the xgb.train function.") 
     } 
     if (!requireNamespace("DiagrammeR", quietly = TRUE)) { 
      stop("DiagrammeR package is required for xgb.plot.tree", 
       call. = FALSE) 
     } 
     allTrees <- xgb.model.dt.tree(feature_names = feature_names, 
      model = model, n_first_tree = n_first_tree) 

     allTrees$Quality <- round(allTrees$Quality, 3) 
     allTrees$Cover <- round(allTrees$Cover, 3) 


     allTrees[, `:=`(label, paste0(Feature, "\\nCover: ", Cover, 
      "\\nGain: ", Quality))] 
     allTrees[, `:=`(shape, "rectangle")][Feature == "Leaf", `:=`(shape, 
      "egg")] 
     allTrees[, `:=`(filledcolor, "Beige")][Feature == "Leaf", 
      `:=`(filledcolor, "Khaki")] 

     nodes <- DiagrammeR::create_node_df(n = length(allTrees[, 
      ID] %>% rev), label = allTrees[, label] %>% rev, style = "filled", width=1.5, 
      color = "DimGray", fillcolor = allTrees[, filledcolor] %>% 
       rev, shape = allTrees[, shape] %>% rev, data = allTrees[, 
       Feature] %>% rev, fontname = "Helvetica", fontcolor="black") 

     edges <- DiagrammeR::create_edge_df(from = match(allTrees[Feature != 
      "Leaf", c(ID)] %>% rep(2), allTrees[, ID] %>% rev), to = match(allTrees[Feature != 
      "Leaf", c(Yes, No)], allTrees[, ID] %>% rev), label = allTrees[Feature != 
      "Leaf", paste("<", Split)] %>% c(rep("", nrow(allTrees[Feature != 
      "Leaf"]))), color = "DimGray", arrowsize = 1, arrowhead = "vee", minlen="5", 
      fontname = "Helvetica", rel = "leading_to", fontsize="15") 

     graph <- DiagrammeR::create_graph(nodes_df = nodes, edges_df = edges, attr_theme=NULL) 
     DiagrammeR::render_graph(graph, width = plot_width, height = plot_height) 
     return(graph) 
}